Merge pull request #1868 from mvdbeek/update_troubleshooting

Replace get_tool_shed_repository_by_tool_shed_name_owner_changeset_re…

lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py

@@ -2,8 +2,6 @@
 import os
 import tempfile
 
-from sqlalchemy import and_
-
 from galaxy.tools.deps.resolvers import INDETERMINATE_DEPENDENCY
 from galaxy.util import listify
 from tool_shed.util import basic_util
@@ -360,34 +358,6 @@ def get_required_repository_package_env_sh_path( self, package_name, package_ver
         env_sh_file_path = os.path.join( env_sh_file_dir, 'env.sh' )
         return env_sh_file_path
 
-    def get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision( self, tool_shed_url, name, owner, changeset_revision ):
-        sa_session = self.app.install_model.context
-        # The protocol is not stored, but the port is if it exists.
-        tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed_url )
-        tool_shed_repository = sa_session.query( self.app.install_model.ToolShedRepository ) \
-                                         .filter( and_( self.app.install_model.ToolShedRepository.table.c.tool_shed == tool_shed,
-                                                        self.app.install_model.ToolShedRepository.table.c.name == name,
-                                                        self.app.install_model.ToolShedRepository.table.c.owner == owner,
-                                                        self.app.install_model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \
-                                         .first()
-        if tool_shed_repository:
-            return tool_shed_repository
-        # The tool_shed_repository must have been updated to a newer changeset revision than the one defined in the repository_dependencies.xml file,
-        # so call the tool shed to get all appropriate newer changeset revisions.
-        text = suc.get_updated_changeset_revisions_from_tool_shed( self.app, tool_shed_url, name, owner, changeset_revision )
-        if text:
-            changeset_revisions = listify( text )
-            for changeset_revision in changeset_revisions:
-                tool_shed_repository = sa_session.query( self.app.install_model.ToolShedRepository ) \
-                                                 .filter( and_( self.app.install_model.ToolShedRepository.table.c.tool_shed == tool_shed,
-                                                                self.app.install_model.ToolShedRepository.table.c.name == name,
-                                                                self.app.install_model.ToolShedRepository.table.c.owner == owner,
-                                                                self.app.install_model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \
-                                                 .first()
-                if tool_shed_repository:
-                    return tool_shed_repository
-        return None
-
     def handle_complex_repository_dependency_for_package( self, elem, package_name, package_version, tool_shed_repository,
                                                           from_tool_migration_manager=False ):
         """
@@ -398,17 +368,15 @@ def handle_complex_repository_dependency_for_package( self, elem, package_name,
         and package_version is being installed.
         """
         handled_tool_dependencies = []
-        tool_shed = elem.attrib[ 'toolshed' ]
-        # The protocol is not stored, but the port is if it exists.
-        tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed )
+        tool_shed_url = elem.attrib[ 'toolshed' ]
         required_repository_name = elem.attrib[ 'name' ]
         required_repository_owner = elem.attrib[ 'owner' ]
         default_required_repository_changeset_revision = elem.attrib[ 'changeset_revision' ]
-        required_repository = \
-            self.get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision( tool_shed,
-                                                                                      required_repository_name,
-                                                                                      required_repository_owner,
-                                                                                      default_required_repository_changeset_revision )
+        required_repository = suc.get_repository_for_dependency_relationship( self.app, tool_shed_url,
+                                                                              required_repository_name,
+                                                                              required_repository_owner,
+                                                                              default_required_repository_changeset_revision )
+        tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed_url )
         tmp_filename = None
         if required_repository:
             required_repository_changeset_revision = required_repository.installed_changeset_revision